System and Method for Scanning a Specimen into a Focus-stacked Scan

ABSTRACT

This disclosure also teaches a system and method for scanning a specimen into a focus-stacked scan. In one embodiment, a method for scanning the specimen into a focus-stacked scan can comprise illuminating the specimen with a light. The specimen can comprise a topography. The depths of the topography can be variable along a z-axis. The method can also comprise dividing the specimen into a plurality of regions. Each of the regions can comprise a regional peak in the topography. Additionally, the method can comprise sampling each of the regions at a plurality of focal planes orthogonal to the z-axis by capturing, at each focal plane, an image of the region. The image can be focused on the focal plane. Lastly, the method can comprise focus-stacking, for each of the region the images within the region, into a focus-stacked image, and stitching together the focus-stacked images.

BACKGROUND

This disclosure relates to a system and method for producing reflectivelight comprising a parabolic mirror, a system and method for producingreflective light comprising a digital light-processing chip, a systemand method for producing transmitted light using a digital lightprocessing chip, an improved method for adjusting white balance, asystem and method for controlling a specimen scanner remotely, a systemand method for scanning a specimen into a focus-stacked scan, a systemand method for scanning a specimen into a multi-dimensional scan, and animproved pyramidal file structure and method of use.

During recent years, oil companies have highly benefitted in applyingmicropaleontological studies for petroleum explorations. Furthermore,applying micropaleontological studies to explorations have resulted inbetter accuracy, less time consumption, and reasonable cost in findingand/or developing oil reserves. Therefore, in association with the highsuccess rate of using micropaleontological studies, demands formicropaleontologists are also increasing. However, at the present thereare limited numbers of licensed specialists that can do this work.Further, while it would be quite advantageous for micropaleontologiststo perform their tasks remotely, such remote work is not presently beingdone for a number of reasons. First, there is presently no specimenscanner known or used within the field of paleontology. Second, thecomponents within a traditional microscope, i.e., the objective lens,reflective light source, stage, and transmitted light source, can bequite bulky, and as such make professional microscopes and potentialspecimen scanners using such parts, difficult to move to offshoreenvironments by a single person. Third, necessary methods for correctingwhite balance often require cumbersome steps such as removing specimensfrom a stage. Fourth, if a specimen were to be completely scanned, aresulting file that contained all the information of the specimen couldbe many gigabytes in size, making it impractical for transfer andviewing. Lastly, creation of a scan often would require input from apaleontologist. However, no system exists for a paleontologist toremotely control a microscope, scanner, or other such device within adrilling environment.

As such it would be useful to have improved reflected and transmittedlight systems. a system and method for controlling a specimen scannerremotely. Further, it would be useful to have an improved method foradjusting white balance. Further, it would be useful to have a systemand method for scanning a specimen into a focus-stacked scan. Further,it would be useful to have a system and method for scanning a specimento create a multidimensional scan. Lastly, it would be useful to have animproved pyramidal file structure and method of use thereof.

SUMMARY

This disclosure teaches a system and method for controlling a specimenscanner remotely.

In one embodiment, a method for controlling a specimen scanner remotelycan comprise the step of communicating with a specimen scanner to anetwork. The specimen scanner can comprise a camera, a stage, one ormore lenses, and one or more light sources. The method can comprise theadditional step of providing a graphical user interface to a remotecomputer connected to the network. The graphical user interface can beoperable to control the camera, choose one of the one or more lenses,and adjust the one or more light sources. The method can furthercomprise the step of receiving instructions from the remote computer,and controlling the specimen scanner based on those instructions.

In another embodiment, a system for controlling a specimen scannerremotely can comprise a server memory and server processor. The servermemory can comprise a server application and a server data store. Theserver processor can, at the instructions of the server application,communicate with a specimen scanner over a network. The specimen scannercan comprise a camera, a stage, one or more lenses, and one or morelight sources. The server application can also provide a graphical userinterface to a remote computer connected to the network. The graphicaluser interface can be operable to control the camera, choose the one ormore lenses, and adjust the one or more light sources. The serverapplication can also receive instruction from the remote computer andcontrol the specimen scanner based on the instructions.

In another embodiment, a computer readable storage medium can store acomputer readable program code. The computer readable program code canbe adapted to be executed to communicate with a specimen scanner over anetwork. The specimen scanner can comprise a camera, a stage, one ormore lenses, and one or more light sources. The code can further beexecuted to provide a graphical user interface to a remote computerconnected to the network. The graphical user interface can be operableto control the camera, choose the one or more lenses, and adjust the oneor more light sources. The code can also be adapted to be executed toreceive instruction from the remote computer and control the specimenscanner based on the instructions.

This disclosure also teaches a system and method for scanning a specimeninto a focus-stacked scan.

In one embodiment, a method for scanning the specimen into afocus-stacked scan can comprise illuminating the specimen with a light.The specimen can comprise a topography. The depths of the topography canbe variable along a z-axis. The method can also comprise dividing thespecimen into a plurality of regions. Each of the regions can comprise aregional peak in the topography. Additionally, the method can comprisesampling each of the regions at a plurality of focal planes orthogonalto the z-axis by capturing, at each focal plane, an image of the region.The image can be focused on the focal plane. Lastly, the method cancomprise focus-stacking, for each of the region the images within theregion, into a focus-stacked image, and stitching together thefocus-stacked images.

In another embodiment, a system for scanning a specimen into afocus-stacked scan can comprise a specimen scanner. The specimen scannercan comprise a camera, a stage capable of supporting a specimen, a lightsource capable of illuminating the specimen, a scanner processor, and ascanner memory. The scanner memory can comprise a scanner application.The scanner application can be capable of directing the light source toilluminate said specimen with a light. The specimen can comprise atopography. The depths of the topography can be variable along a z-axis.Furthermore, the scanner application can be capable of dividing thespecimen into a plurality of regions. Each of the regions can comprise aregional peak in the topography. The method can also comprise samplingeach of the regions at a plurality of focal planes orthogonal to thez-axis by capturing with the camera, at each focal plane, an image ofthe region. The image can be focused on the focal plane. Moreover, thescanner application can be capable of focus-stacking, for each of theregion the images within the region, into a focus-stacked image, andstitching together the focus-stacked images.

In another embodiment, a method for scanning a specimen can comprise thesteps of aiming a camera at a plurality of regions of a specimen, oneregion at a time, and illuminating the specimen with one or more lights.The method can also comprise capturing at each of the regions for eachof the lights, at a plurality of focal planes for each focal plane, animage of the region. The image can be focused on the focal plane.Additionally, the method can comprise focus-stacking, for each of theregion the images captured with a common light of one or more lights,within the region, into a focus-stacked images. Lastly, method cancomprise stitching together the focus-stacked images captured with thecommon light.

This disclosure also teaches a system and method for scanning a specimento create a multidimensional scan.

In one embodiment, a method for scanning the specimen to create amultidimensional scan can comprise illuminating a specimen with a lightand dividing the specimen into a plurality of regions. The specimen cancomprise a topography. The depths of the topography can be variablealong a z-axis. Each of the regions can comprise a minimum depth and amaximum depth. The topography is between the minimum depth and themaximum depth. The method can also comprise sampling each of the regionsat a plurality of focal planes orthogonal to the z-axis by capturing, ateach focal plane, an image of the region. The image can be focused onthe focal plane. Lastly, the method can comprise stitching together theimages into a dimensional image for each of the focal planes.

In another embodiment, a system for scanning the specimen to create amultidimensional scan can comprise a specimen scanner. The specimenscanner can comprise a camera, a stage capable of supporting thespecimen, a light source capable of illuminating the specimen, a scannerprocessor, and a scanner memory. The scanner memory can comprise ascanner application. The scanner application can be capable ofilluminating the specimen with a light, and dividing the specimen into aplurality of regions. The specimen can comprise a topography. The depthsof the topography can be variable along a z-axis. Each of the regionscan comprise a minimum depth and a maximum depth. The topography isbetween the minimum depth and the maximum depth. Additionally, thescanner application can be capable of sampling each of the regions at aplurality of focal planes orthogonal to the z-axis by capturing, at eachfocal plane, an image of the region. The image can be focused on thefocal plane. Lastly, the scanner application can be capable of stitchingtogether the images into a dimensional image for each of the focusplanes.

In another embodiment, a method for scanning a specimen can comprise thesteps of aiming a camera at a plurality of regions of a specimen, oneregion at a time, and illuminating the specimen with one or more lights.The method can also comprise capturing at each of the regions for eachof the lights, at a plurality of focal planes for each focal plane, animage of the region. The image can be focused on the focal plane.Lastly, the method can comprise stitching together the images focused ona common focal plane and captured with a common light.

This disclosure also teaches an improved pyramidal file structure andmethod of use thereof.

A pyramidal file structure can comprise a body and a header. The bodycan comprise a plurality of layers. The layers divided into tiles. Eachof the tiles can be capable of comprising a plurality of images. Theheader that can define a layer plan, a tile plan, and an image plan.

A method of storing a scan within a pyramidal file structure cancomprise defining in a header of a pyramidal file structure a pyramidaldata structure. The header can define a layer plan, a tile plan, and animage plan. The method can also comprise storing in each tile of thepyramidal data structure of the pyramidal file structure a plurality ofimages. The pyramidal data structure can comprise a plurality of layers,each of the layers comprising one or more of the tiles.

A method of receiving a pyramidal file structure can comprise the stepof transmitting a header of a pyramidal file structure. The header candefine a layer plan, a tile plan, and an image plan, of a pyramidal datastructure of the pyramidal file structure. The method can also comprisethe step of building the pyramidal data structure based on the layerplan, tile plan, and the image plan. Additionally, the method cancomprise the step of transmitting one or more tiles to store within thepyramidal data structure. Each of the one or more tiles can comprise aplurality of images.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates a specimen scanner.

FIG. 2 illustrates a schematic block diagram of a specimen scanneraccording to an embodiment of the present disclosure.

FIG. 3 illustrates an exemplary configuration of a specimen scanner,with a display and one or more input devices.

FIG. 4 illustrates another exemplary configuration of a specimenscanner, with a computer.

FIG. 5 illustrates another exemplary configuration of a specimenscanner.

FIG. 6A illustrates a schematic diagram of a server according to anembodiment of the present disclosure.

FIG. 6B illustrates a schematic diagram of a computer according to anembodiment of the present disclosure

FIG. 7 illustrates a first embodiment of a reflective light sourcesystem.

FIG. 8 illustrates a front view of the first disclosed embodiment ofreflective light source system.

FIG. 9 illustrates a second embodiment of a reflective light sourcesystem.

FIG. 10 illustrates a first digital light-processing (DLP) chip as wellas an exploded view of a reflective digital microscopic mirror (DMM)array.

FIG. 11 illustrates a representation of reflective DMMs at an “OFF”state.

FIG. 12 illustrates a representation of reflective DMMs in an “ON”state.

FIG. 13 illustrates a display showing a specimen illuminated by aninitial light pattern from a reflective light source system comprising afirst DLP chip.

FIG. 14 illustrates a reflective DMM array comprising a reflective ONDMMs and OFF DMMs set to produce a subsequent illumination pattern.

FIG. 15 illustrates a display showing areas of interest illuminated by asubsequent illumination pattern from a reflective light source system.

FIG. 16 illustrates a reflective DMM array arranged to produce anupdated subsequent lighting pattern.

FIG. 17 illustrates a display showing areas of interest illuminated byan updated subsequent pattern from a reflective light source system.

FIG. 18 illustrates an embodiment of a transmitted light source systemthat uses a digital light-processing (DLP) chip.

FIG. 19 illustrates a representation of one of transmitted light DMMs atan “OFF” state.

FIG. 20 illustrates a second DLP chip producing various lightingpatterns to imitate a condenser.

FIG. 21 illustrates an embodiment of a stage system.

FIG. 22 illustrates a top view of a stage.

FIG. 23 illustrates a bottom view of a stage.

FIG. 24 illustrates a glass slide mounted within a stage.

FIG. 25 illustrates a glass slide mounted onto a stage at a verticalposition.

FIG. 26 illustrates a preferred method of setting white balance using astage.

FIG. 27 illustrates a graphical user interface configured to control aspecimen scanner during a real-time image data display of a specimen.

FIG. 28 illustrates a graphical user interface configured to allow userto setup scanning of a specimen.

FIG. 29 illustrates a graphical user interface displaying a scan order.

FIG. 30 illustrates a glass slide.

FIG. 31 illustrates a side view of a glass slide.

FIG. 32 illustrates a region that is sampled by a scanner application.

FIG. 33 illustrates another region that is sampled by a scannerapplication.

FIG. 34 illustrates an exemplary method for scanning a specimen forcreating a focus-stacked scan.

FIG. 35 illustrates another exemplary method for scanning a specimen forcreating a focus-stacked scan.

FIG. 36 illustrates a glass slide.

FIG. 37 illustrates another exemplary method for scanning a specimen forcreating a focus-stacked scan.

FIG. 38 illustrates focus planes within a specimen.

FIG. 39 illustrates an exemplary region illuminated at various lightsettings, sampled with a sampling distance (Δz) using light setting withshortest wavelength.

FIG. 40 illustrates an exemplary region illuminated at various lightsetting, sampled with various sampling distance (Δz) relative to eachlight setting.

FIG. 41 illustrates an exemplary method for scanning a specimen using amulti-dimensional scanning.

FIG. 42 illustrates another exemplary method for scanning a specimen ateach focal plane using multi-dimensional scanning.

FIG. 43 illustrates a pyramidal data structure.

FIG. 44 illustrates one embodiment of a multi-modal pyramidal datastructure.

FIG. 45 illustrates one embodiment of a multi-dimensional pyramidal datastructure.

FIG. 46 illustrates one embodiment of multi-modal multi-dimensionalpyramidal data structure.

FIG. 47 illustrates another embodiment of multi-modal multi-dimensionalpyramidal data structure.

FIG. 48 illustrates a pyramidal file structure capable of enclosing apyramidal data structure having one or more modes, and a plurality ofdimensions.

FIG. 49 illustrates a viewer application allowing user to view scans ofa specimen within a pyramidal data structure.

FIG. 50A illustrates an entire specimen being viewed.

FIG. 50B illustrates a specimen being magnified by adjusting amagnifier.

FIG. 50C illustrates a specimen being magnified by further adjusting amagnifier.

FIG. 50D illustrates a specimen being completely magnified by furtheradjusting a magnifier to its maximum position.

FIG. 51 illustrates how image data can be transferred from a localaccess to a remote access.

FIG. 52 illustrates magnifying a selected area of specimen on a remoteaccess.

FIG. 53 illustrates fully magnifying a selected area from a remoteaccess.

FIG. 54 illustrates selecting a different area to view from a remoteaccess.

FIG. 55A illustrates a viewer application viewing a sub-image focused ona focal plane near a region peak.

FIG. 55B illustrates a viewer application viewing a sub-image focused ona focal plane between a regional peak and a maximum depth.

FIG. 55C illustrates a viewer application viewing a sub-image focused ona focal plane near a maximum depth.

FIG. 55D illustrates a viewer application switching modes using modeselection when viewing a multi-modal multi-dimensional pyramidal filestructure on a display.

DETAILED DESCRIPTION

Described herein is a system and method for producing reflective lightcomprising a parabolic mirror, a system and method for producingreflective light comprising a digital light-processing chip, a systemand method for producing transmitted light using a digital lightprocessing chip, an improved method for adjusting white balance, asystem and method for controlling a specimen scanner remotely, a systemand method for scanning a specimen into a focus-stacked scan, a systemand method for scanning a specimen into a multi-dimensional scan, and animproved pyramidal file structure and method of use. The followingdescription is presented to enable any person skilled in the art to makeand use the invention as claimed and is provided in the context of theparticular examples discussed below, variations of which will be readilyapparent to those skilled in the art. In the interest of clarity, notall features of an actual implementation are described in thisspecification. It will be appreciated that in the development of anysuch actual implementation (as in any development project), designdecisions must be made to achieve the designers' specific goals (e.g.,compliance with system- and business-related constraints), and thatthese goals will vary from one implementation to another. It will alsobe appreciated that such development effort might be complex andtime-consuming, but would nevertheless be a routine undertaking forthose of ordinary skill in the field of the appropriate art having thebenefit of this disclosure. Accordingly, the claims appended hereto arenot intended to be limited by the disclosed embodiments, but are to beaccorded their widest scope consistent with the principles and featuresdisclosed herein.

FIG. 1 illustrates a specimen scanner 100. Specimen scanner 100 cancomprise a camera system 101, a reflective light source system 102, anobjective lens system 103, a stage system 104, and/or a transmittedlight source system 105. Camera system 101 can comprise a camera 106.Camera 106 can be any optical instrument capable of capturing digitalimages. In one embodiment, camera 106 can comprise an interferometer113. Reflective light source system 102 can be one of the systemsdescribed further herein. Alternatively, reflective light source system102 can be any reflective light source known in the art. Reflectivelight source system 102 can be placed below camera 106. Objective lenssystem 103 can be positioned below reflective light source system 102.Objective lens system 103 can comprise one or more objective lenses 107capable of magnifying a specimen. Stage system 104 can comprise a stage108, and an actuating system 109. Stage 108 can be a platform forspecimens, and is in visual alignment with camera 106, and object lens107. Actuating system 109 can position stage 108. In one embodiment,actuating system 109 can position stage 108 left and right, and forwardand backward (XY). In another embodiment, actuating system 109 canposition stage 108 left and right, forward and backward, and up and down(XYZ). Transmitted light source system 105 can be one of the systemsdescribed further herein. Alternatively, transmitted light source system105 can be any known in the art. Transmitted light source system 105 cancomprise a transmitted light source 110. Further, specimen scanner 100can mount a glass slide 111 onto stage 108. Glass slide 111 can comprisea specimen 112. One example of glass slide 111 and specimen 112 is apetrographic thin section.

FIG. 2 illustrates a schematic block diagram of specimen scanner 100according to an embodiment of the present disclosure. Specimen scanner100 can include at least one processor circuit, for example, having ascanner processor 201 and a scanner memory 202, both of which can becoupled to a first local interface 203. First local interface 203 cancontrol a display for the user, which can allow user to view and/orinteract with specimen scanner 100. First local interface 203 cancomprise, for example, a data bus with an accompanying address/controlbus or other bus structure as can be appreciated.

Stored in scanner memory 202 described herein above are both data andseveral components that are executable by scanner processor 201. Inparticular, stored in scanner memory 202 and executable by scannerprocessor 201 are scanner application 204, and potentially otherapplications. Also stored in scanner memory 202 can be a data store 205and other data. In addition, an operating system can be stored inscanner memory 202 and executable by scanner processor 201.

FIG. 3 illustrates an exemplary configuration of specimen scanner 100,with a display 302 and one or more input devices 301. Display 302 can beany device capable of displaying image data that is processed byspecimen scanner 100. In one embodiment, monitor 302 can be a touchscreen. In such embodiment, monitor 302 can function as an input device.Input devices 301 can be any peripherals that can convert user's actionand/or analog data into digital electronic signals that specimen scanner100 can process. Input device 301 can include, but is not limited to amouse, keyboard, and/or track ball. In such configuration, image datathat is viewed through display 302 can be selected, controlled, and/ormanipulated through input device 301.

FIG. 4 illustrates another exemplary configuration of specimen scanner100, with a computer 401. Computer 401 can comprise drivers or otherspecialized software to interface with specimen scanner 100. Examples ofcomputers 401 can include, but are not limited to, a desktop computer,laptop, tablet, or smart device. In such embodiment, image data capturedby specimen scanner 100 can be viewed, recorded, controlled, and/orstored within computer 401.

FIG. 5 illustrates another exemplary configuration of specimen scanner100. In this embodiment, specimen scanner 100 can connect to one or morecomputers 401, and one or more servers 501 through a network 502. Server501 represents at least one, but can be many servers, each connected tonetwork 502 capable of performing computational tasks, and storing datainformation. Network 502 can be a local area network (LAN), a wide areanetwork (WAN), a piconet, or a combination of LANs, WANs, and/orpiconets. One illustrative LAN is a network within a single business.One illustrative WAN is the Internet. In the preferred embodiment,network 502 will comprise the Internet. In this embodiment, input datathat is processed by specimen scanner 100 can be accessible to computers401 through server 501 that is within network 502.

FIG. 6A illustrates a schematic diagram of server 501 according to anembodiment of the present disclosure. Server 501 includes at least oneprocessor circuit, for example, having a server processor 601 and aserver memory 602, both of which can be coupled to a second localinterface 603. To this end, server 501 can comprise, for example, atleast one server, computer or like device. Server memory can compriseserver application 604 and server data store 605. Second local interface603 can comprise, for example, a data bus with an accompanyingaddress/control bus or other bus structure as can be appreciated. Inparticular, stored in the server memory 602 and executable by serverprocessor 601 are server application 604, and potentially otherapplications. Also stored in server memory 602 can be server data store605 and other data. In addition, an operating system can be stored inserver memory 602 and executable by server processor 601.

FIG. 6B illustrates a schematic diagram of computer 401 according to anembodiment of the present disclosure. Computer 401 includes at least oneprocessor circuit, for example, having computer processor 606 andcomputer memory 607, both of which can be coupled to third localinterface 608. Computer memory 607 can comprise computer application 609and computer data store 610. Third local interface 608 can comprise, forexample, a data bus with an accompanying address/control bus or otherbus structure as can be appreciated. In particular, stored in thecomputer memory 607 and executable by computer processor 606 arecomputer application 609, and potentially other applications. In oneembodiment, computer application 609 can be a web browser that gives auser the ability to interface with server application 604 or scannerapplication 204. Further, in one embodiment, scanner application 204,server application 604 and computer application 209 can have sharedresponsibilities to complete methods taught in this disclosure. Alsostored in computer memory 607 can be computer data store 610 and otherdata. In addition, an operating system can be stored in computer memory607 and executable by computer processor 606.

FIG. 7 illustrates a first embodiment of reflective light source system102. In microscopy, a reflective light source illuminates a specimen byreflecting light off the specimen. In this embodiment, reflective lightsource system 102 can comprise a parabolic mirror 703, a second mirror704, and a plurality of light-emitting diodes (LEDs) 705. Light guide701 can connect a dichroic mirror 707 with an aperture 702. In apreferred embodiment, light guide 701 can be a liquid light guide.Aperture 702 can be positioned at the vertex of parabolic mirror 703. Inone embodiment, second mirror 704 can be placed at a point equidistantfrom both aperture 702 and a parabolic focal point 706. LEDs 705 can bepointed at parabolic mirror 703 in a direction parallel to a line thatpasses through both the vertex of parabolic mirror 703, and parabolicfocal point 706. Thus, when the light on a LED 705 is switched on, thelight can travel towards parabolic mirror 703. The light emitted by LEDs705 can then reflect off parabolic mirror 703 in a direction towardparabolic focal point 706. However, the light will hit second mirror 704before reaching parabolic focal point 706. In such structure, the lightthat hits second mirror 704 can reflect off second mirror 704 and traveltoward aperture 702. At aperture, the light can enter light guide 701,and then travel through light guide 701 to dichroic mirror 707. Fromthere, light can be redirected to specimen 112.

FIG. 8 illustrates a front view of the first disclosed embodiment ofreflective light source system 102. Aperture 702 can be positioned atthe vertex of parabolic mirror 703, while each LED 705 can be mounted infront of parabolic mirror 703. In one embodiment, LEDs 705 can be placedin a circular pattern. Additionally, LEDs 705 can be parallel with oneanother. In one embodiment, one LED 705 can be turned on at a time. Inanother preferred embodiment, each LED 705 can be one or more LEDs,which can increase the intensity of the light from LED 705. Each LEDs705 can have different characteristics, such as color, and intensity. Asan example, LEDs 705 can comprise of a yellow LED 705 a, a red LED 705b, a white LED 705 c, a green LED 705 d, a blue LED 705 e, a magenta LED705 f, a purple LED 705 g, and an orange LED 705 h.

In one scenario, the user can select LED 205, comprising a certaincharacteristic such as a color. In this example, the user can select“yellow” through computer 401. Scanner processor 201 can receive thecolor that the user selected and then send an instruction to specimenscanner 100 to switch ON a first LED 705 a. First LED 705 a is switchedon, which produces yellow light to reflect off parabolic mirror 703.Yellow light is then reflected towards aperture 702 and travels throughlight guide 701. The light reflects of dichroic mirror 707 andilluminates the specimen with yellow light. To illuminate the specimenin a different color, the user can again select a different colorthrough computer 401. In this case, the user selects color the “white”.Scanner processor 201 can receive the color selected, and then sends asignal to switch OFF yellow LED 705 a, and then turns on white LED 705c.

FIG. 9 illustrates a second embodiment of reflective light source system102. In this embodiment, reflective light source system 102 can comprisea reflective light source 901, a reflective light absorber 902, and afirst digital light-processing (DLP) chip 903. Reflective light source901 can be a device capable of emitting light, which can include but isnot limited to a LED, a laser, and/or a fluorescent light. Reflectivelight absorber 902 can be any device capable of absorbing the lightemitted from reflective light source 901. An example of DLP chip 903 isthe DLP700 produced and marketed by the company Texas Instruments®. In apreferred embodiment, first DLP chip 903 can be placed in front ofdichroic mirror 707, while reflective light absorber 902 and reflectivelight source 901 are positioned at an angle away from first DLP chip903.

FIG. 10 illustrates first DLP chip 903 as well as an exploded view of areflective digital microscopic mirror (DMM) array 1001. Reflective DMMarray 1001 comprises a plurality of reflective digital microscopicmirrors DMMs 1002 that are arranged side by side to form rows andcolumns.

FIG. 11 illustrates a representation of reflective DMM 1002 at an “OFF”state 1002 a. At this state, reflective DMM 1002 is laying flat toreflect off light towards the direction of reflective light absorber902. Thus, the light reflected off reflective DMM 1002 in an “OFF” state1002 a can make the pixel appear dark.

FIG. 12 illustrates a representation of reflective DMM 1002 in an “ON”state 1002 b. By tilting or by lying flat, reflective DMM 1002 canreflect off light from reflective light source 901 to either thedirection of reflective light absorber 902 or the direction towardsdichroic mirror 707. In ON state 1002 b, the reflected light fromreflective DMM 1002 can make the pixel appear illuminated. In FIG. 12,reflective DMM 1002 is tilted to reflect light toward dichroic mirror707. Together, DMMs 1002 in an ON state 1002 b transmit light throughdichroic mirror 707 and onto the surface of specimen 112. Depending onwhich DMMs 1002 are illuminated, all or a portion of specimen 112 can beilluminated. First DLP chip 903 can give reflective light source system102 great flexibility and control regarding what specific portions ofspecimen 112 are illuminated and at what intensity.

FIG. 13 illustrates display 302 showing specimen 112 illuminated by aninitial light pattern 1301 from reflective light source system 102comprising first DLP chip 903. In some situations, it may beadvantageous for a user to illuminate specific areas of interest in aspecimen, while not illuminating other areas. In one exemplary method, auser can choose which areas are illuminated, illuminated areas 1302 andwhich areas are not illuminated, non-illuminated areas 1303. In suchmethod, a user can mount glass slide 111 on stage 108 to view specimen112. Camera 106 can capture glass slide 111 in real time. Initially, allor a significant portion of specimen 112 or the presently viewed portionof specimen 112 can be illuminated by reflective light source system102.

Next, the user can select which portions of specimen 112 are to beilluminated. The user can make such selections using local input devices301, as shown in FIG. 3, a local computer as shown in FIG. 4, or aremote computer 401 as shown in FIG. 5. In one embodiment, suchselection can be completely manual. In another embodiment, scannerapplication 204 can automate all or portions of the selection process.In an example manual embodiment, a user can select to illuminate one ormore areas of interest 1304 in specimen 112 by defining areas ofinterest 1304 using input devices 301 attached to specimen scanner 100or a computer 401. One exemplary way to define an area is to trace anarea. In an example of an automated embodiment, a user may select aparticular object, and scanner application 204, using color information,edge detection techniques, and/or shape recognition methods, candetermine particular areas of illumination. In another embodiment,scanner application 204 can predict, without user selection, areas ofinterest for illumination, using edge detection, color recognition,shape recognition, and/or intelligent predictions based on previousillumination requests by a user.

Once areas of interest 1304 are selected, scanner processor 201 can sendsignal to first DLP chip 903 to produce the desired illumination.Scanner application 204 can determine which reflective DMMs 1002 need tobe turned on and which reflective DMMs 1002 need to be turned off. Oneparticular issue with determining which DMMs need to be turned on toilluminate a particular area of glass slide 111, is that each objectivelens 107 disperses light differently. In one embodiment, dispersionpatterns for different objective lens 107 can be stored in scannermemory 202. Using dispersion patterns, scanner application 204 cancalculate which reflective DMMs 1002 can be turned on to illuminateareas of interest 1304 on display 302. In another embodiment, scannerapplication 204 can determine which DMMs 1002 need to be turned on usingfeedback techniques, as described below and shown in FIGS. 14-17

FIG. 14 illustrates reflective DMM array 1001 comprising reflective ONDMMs 1002 a and OFF DMMs 1002 b set to produce a subsequent illuminationpattern 1401. In one embodiment, such subsequent illumination patterncan be based on mapping to display 302 to first DLP chip 903. Oncescanner application 204 creates subsequent illumination pattern 1401,first DLP chip 903 can project such illumination pattern on to specimen112.

FIG. 15 illustrates display 302 showing areas of interest 1304illuminated by subsequent illumination pattern 1401 from reflectivelight source system 102. Subsequent illumination pattern 1401 can haveone or more over-illuminated areas 1502, one or more under-illuminatedareas 1503, one or more correctly illuminated areas 1504, and one ormore correctly non-illuminated areas 1505. Over-illuminated areas 1502can be caused by some reflective DMMs 1002 incorrectly in an ON state.Under-illuminated areas 1503 can be caused by some reflective DMMs 1002incorrectly in an OFF state. In such scenario, scanner application 204can compare the light pattern on display 302 from subsequentillumination pattern 1401 to the light pattern on display 302 frominitial illumination pattern 1301. By comparing the two light patternsin relation to the location of areas of interest 1304, scannerapplication 204 can determine over-illuminated areas 1502 andunder-illuminated areas 1503. Scanner application 204 can then adjustreflective DMMs 1002 to produce an updated subsequent illuminationpattern.

FIG. 16 illustrates reflective DMM array 1001 arranged to produce anupdated subsequent lighting pattern 1601. The signals sent by scannerprocessor 201 to reflective DMM array 1001 can be based from updatedsubsequent illumination pattern 1601 that is determined by scannerapplication 204. The updated illumination pattern can be projected byfirst DLP chip 903 to specimen 112.

FIG. 17 illustrates display 302 showing areas of interest 1304illuminated by updated subsequent pattern 1601 from reflective lightsource system 102. In this scenario, the illuminated light pattern fromupdated subsequent pattern 1601 can be projected onto specimen 112. Suchiterative techniques can be performed by scanner application 204 untilthe existence of over-illuminated areas 1502 and/or under illuminatedareas 1503 are within a predetermined acceptable threshold.

FIG. 18 illustrates an embodiment of transmitted light source system 105that uses a digital light-processing (DLP) chip. Transmitted lightsource system 105 can comprise a transmitted light source 1801, atransmitted light absorber 1802, and a second digital light-processing(DLP) chip 1803. In a preferred embodiment, second DLP chip 1803 can beplaced below stage 108, while transmitted light source 1801, andtransmitted light absorber 1802 can be positioned at an angle away fromsecond DLP chip 1803. Further, second DLP chip 1803 can comprise atransmitted light DMM array 1804. Transmitted light DMM array 1804 cancomprise a plurality of transmitted light DMMs 1805 that are arrangedside by side to form rows and columns. By tilting or by lying flat,transmitted light DMMs 1805 can reflect off light from transmitted lightsource 1801 and transmit light to either the direction of transmittedlight absorber 1802 or the direction towards stage 108. In FIG. 18,transmitted light DMM 1805 is tilted to transmit light towards stage108. At this state, DMMs 1805 in an ON state can transmit light towardsstage 108 and through the surface of specimen 112. In this state, thelight is focused towards specimen 112 to provide controlledillumination.

FIG. 19 illustrates a representation of one of transmitted light DMM1805 at an “OFF” state. In this state, transmitted light DMM 1805 islying flat to transmit light towards the direction of transmitted lightabsorber 1802. The light transmitted from transmitted light DMMs 1805 atan OFF state can make the pixel appear dark.

FIG. 20 illustrates second DLP chip 1803 producing various lightingpatterns to imitate a condenser. In a preferred embodiment, transmittedlight DMM array 1804 can produce illuminations that are based frompreset patterns that are stored within DMM settings. In such embodiment,light produced from transmitted light DMM array 1804 can imitate lightproduced from various condenser settings of a microscope. In oneembodiment, input device 301 or computer 401 can be used to select adesired lighting pattern. Once the desired lighting pattern is selected,scanner processor 201 can send signal to transmitted light DMMs array1804, which can allow transmitted light DMMs 1805 to produce anillumination according to one of the stored DMM settings associated withsuch lighting pattern. The pre-determined illumination for each lightingpattern that is stored within scanner memory 202 can allow scannerapplication 204 to determine, which transmitted light DMM's 1805 can beat an “ON” state or at an “OFF” state. The light produced fromtransmitted light DMMs 1805 can be transmitted towards the direction ofstage 108. The transmitted light can then pass through glass slide 111and illuminate specimen 112.

FIG. 21 illustrates an embodiment of stage system 104. Stage system 104can comprise stage 108, actuating system 109, a stage-housing 2101, anda mounting structure 2102. Stage-housing 2101 can enclose actuatingsystem 109. Actuating system 109 can control position of stage 108 alongX-axis, Y-axis, and Z-axis. In one embodiment, XY-positioner can use apiezo motor while Z-positioner can use a voice coil motor. This canallow actuating system 109 to provide better precision and speed.Further, mounting structure 2102 can be connected to stage-housing 2101and can be positioned below stage 108. Additionally, mounting structure2102 can comprise an opening that allows light to pass through. Theopening in mounting structure 2102 can allow light from transmittedlight source 110 be transmitted towards stage 108.

FIG. 22 illustrates a top view of stage 108. Stage 108 can comprise agrasp point 2202 and a connection point 2203. Stage 108 can comprise astage opening 2204. In one embodiment, stage opening 2204 can be across-shaped orifice that is placed at the center of stage 108. In suchstructure, glass slide 111 can be mounted horizontally or verticallywithin stage opening 2204. Each opposite ends of stage opening 2204 cancomprise slide supports 2205. Slide supports 2205 can secure glass slide111 in place. Grasp point 2202 can be a portion for a user to manuallymanipulate. Connection point 2203 can be placed at one side of stage108, and can connect stage 108 to actuating system 109.

FIG. 23 illustrates a bottom view of stage 108. In one embodiment,connection point 2203 can comprise magnets 2302. Magnets 2302 can affixstage 108 to actuating system 109. In one embodiment, magnets can befixed into a recess 2301 at connection point 2203.

FIG. 24 illustrates glass slide 111 mounted within stage 108. Glassslide 111 can be mounted over stage opening 2204. Because of thecross-shaped form of stage opening 2204, placing glass slide 111 ontostage opening 2204 can leave spaces 2401 at opposite sides of stageopening 2204. In FIG. 24, placing glass slide 111 onto stage opening2204 in a horizontal position can leave spaces 2401 at the top and atthe bottom of glass slide 111. Spaces 2401 can then allow transmittedlight to pass by glass slide 111. Sometimes, such as in petrographicscenarios, it is necessary to view slides in both a horizontal andvertical orientation.

FIG. 25 illustrates glass slide 111 mounted onto stage 108 at a verticalposition. In this orientation, glass slide 111 can be placed onto stageopening 2204 in a vertical position leaving spaces 2401 at the sides ofglass slide 111, which can allow transmitted light to pass by glassslide 111.

FIG. 26 illustrates a preferred method of setting white balance usingstage 108. In the method, a user can place glass slide 111 within stage108. Stage 108 can comprise space 2401 along at least one side of glassslide 111. Light from transmitted light source 1801 can pass throughspace 2401. In one embodiment, transmitted light source 1801 can use awhite LED light. Next, scanner application 204 can adjust camera 106and/or stage 108 so that camera 106 can focus on space 2401. Image ofspace 2401 can then be captured through camera 106, which can produce awhite image. Using known methods, scanner application 204 can calculatethe correction factors based from the white image. Once white balance isset, the scanner application 204 can adjust camera 106 and/or stage 108to focus camera 106 on specimen 112. Scanner application 204 can thenadjust white balance on specimen 112 using the correction factors.Lastly, the user can capture images of specimen 112 using the adjustedwhite balance settings.

FIG. 27 illustrates a graphical user interface 2700 configured tocontrol specimen scanner 100 during a real-time image data display ofspecimen 112. Graphical user interface 2700 can be a part of scannerapplication 204, server application 604, or computer application 609. Inthis embodiment, specimen scanner 100 can be controlled from anothercomputer 401. In one embodiment, computer 401 and scanner 100 cancommunicate directly. In another embodiment, communication betweencomputer 401 and scanner 100 can be managed by server application 604.By controlling specimen scanner 100, the user at a local or remotelocation can view image data of specimen 112 in real time. Further inone embodiment, real-time image data of specimen 112 can be a video. Inanother embodiment, real-time image data of specimen can be an image.

In one embodiment, graphical user interface 2700 can comprise a lenssetting 2701, a focus control 2702, a panning control 2703, a lightsettings 2704, a white balance control 2705, a viewing area 2706, and abegin-scan button 2707. Lens setting 2701 can allow user to selectmagnification of the image of specimen 112. In one embodiment,magnifying specimen 112 can result in choosing a particular objectivelens 107. Focus control 2702 can allow user to adjust the focus ofscanner 100 on specimen 112. In one embodiment, focus control can resultin moving stage 108 along its z-axis. In another embodiment, camera 106can move instead of stage 108. Panning control 2703 can allow user tomove image of specimen 112. In one embodiment panning specimen 112 canresult in moving stage 108 along its x-axis and y-axis. In anotherembodiment, panning specimen 112 can result in moving camera 106.

In one embodiment light settings 2704 can further comprise a reflectivelight controller 2708, and a transmitted light controller 2709.Reflective light controller 2708 can allow user to control reflectivelight source system 102, such as by selecting a color of light to use toilluminate specimen 112. Further in one embodiment reflective lightcontroller 2708 can allow a user to control the illumination intensityof the reflected light.

Transmitted light controller 2709 can allow user to control transmittedlight source 110, such as by turning transmitted light source system 105on or off. In other embodiments, transmitted light controller 2709 canprovide more controls such as condenser controls, or light shaping toimitate condenser settings.

White balance control 2705 can comprise an auto-adjust control 2710. Inone embodiment, auto-adjust control 2710 can be a button. In suchembodiment, pressing auto-adjust control 2710 can automatically applycolor balance to specimen 112 according the method described earlier inthis disclosure or by any other method known in the art.

Viewing area 2706 can allow user to view specimen 112 in real-time usingthe settings selected by the user. As an example shown in FIG. 27, theuser can choose to view specimen 112 using the following settings:select lens setting 2701 at 5× magnification, select reflective lightwhite checkbox, and select transmitted light ON. Viewing area 2706 canthen show specimen 112 using the selections made on control settings.This can allow the user to inspect image of specimen 112 before a scan.One reason a user may want to view specimen in real time is to prepareto scan specimen 112, as described further in this disclosure. Once auser has made certain determinations regarding specimen 112, the usercan begin the scanning process, in one embodiment by clicking a “Beginscan” button 2707, which can allow user to start setting up various scansettings to use in scanning a selected portion or an entire portion ofspecimen 112.

FIG. 28 illustrates graphical user interface 2700 configured to allowuser to setup scanning of specimen 112. In one embodiment, graphicaluser interface 2700 can comprise a scan-type selection 2801, lenssetting 2701, light settings 2704, white balance control 2705, ascanning area 2802 and an add-to-scan button 2803.

To perform a scan or set of scans, a user can select which objectivelens 107 can be used for the scan. A user may additionally selectwhether or not scanner 100 will perform a white balance adjustmentbefore scanning. In one embodiment, such selections can be global. Ifglobal, such decisions will be implemented for each scan in a set ofscans. Graphical user interface 2700 can allow for additionalconfigurations. Scan-type selection 2801 can allow user to select howspecimen 112 can be scanned. In one embodiment, user can either select afocus-stacked selection 2801 a, or a multi-dimensional selection 2801 b.If the user selects focus-stacked selection 2801 a, a focus-stacked scancan be performed when scanning specimen 112, as described further inthis disclosure. If the user selects multi-dimensional selection 2801 b,a multi-dimensional scan can be performed, as described further in thisdisclosure. In one embodiment, user can select both. In such instance,scanner application 204 can create both scan types from a single scan ofspecimen 112 or from two scans. Light settings 2704 can allow user toselect the color of light to use when illuminating specimen 112. Assuch, user can select reflective light controller 2708 and/ortransmitted light controller 2709. Under reflective light controller2708, a user can choose from a plurality of light colors. Undertransmitted light controller 2709 and reflective light controller 2708,in one embodiment, user can also make changes to light shape and/orintensity.

In one embodiment, an image of specimen 112 can be shown on scanningarea 2802 according to the settings selected by the user. As such,scanning area 2802 can allow user to view an image of specimen 112before scan. After selecting the settings for a scan, the user can clickon add-to-scan button 2803 to add a scan setting to use in scanningspecimen 112. In one embodiment, the user can repeat this process tocreate a set of scans of specimen 112 for specimen scanner 100 toperform in one session.

FIG. 29 illustrates graphical user interface 2700 displaying a scanorder 2901. Scan order 2901 can comprise a summary of scans about to beperformed by specimen scanner 100. If the user is satisfied, then he orshe can initiate scanning by, in one embodiment, clicking astart-scanning button 2902.

FIGS. 30-42 illustrate various systems and methods for scanning specimen112.

FIG. 30 illustrates glass slide 111. To capture entire specimen 112,scanner application 204 can divide specimen 112 into a plurality ofregions 3001 based on lens settings 2701. Camera 106 can then captureimage/s of each region 3001 according to the methods described below.

FIGS. 31-37 illustrate methods for producing a focus-stacked scan. In afocus-stacked scan embodiment, images of selected region 3001 can becaptured by camera 106 at different focal planes. These images capturedat different focal planes can be combined to create a singlefocus-stacked image with greater depth of focus using a novelfocus-stacking technique.

FIG. 31 illustrates a side view of glass slide 111 and specimen 112.Glass slide 111 can comprise specimen 112 mounted between a top glassslide 3101, and a bottom glass slide 3102. Specimen 112 can comprisetopography 3103. Each region 3001 can comprise a regional peak 3105, andmaximum depth 3106. In each region 3001, regional peak 3105 can be thehighest point in topography 3103 in that particular region 3001. Maximumdepth 3106 can be the lowest sampling position. In one embodiment,maximum depth 3106 can be predetermined. In one embodiment, maximumdepth 3106 can be the top of bottom glass slide 3102. During thescanning process, interferometer 113 can shoot a laser at each region3001 and measure the time it takes before interferometer 113 can receivea reflection of the laser. The first reflections interferometer 113 canreceive can come from regional peak 3105 of selected region 3001. Basedfrom interferometer 113's measurement result, scanner application 204can determine the highest point camera 106 needs to focus on whencapturing images along the z-axis of each region 3001. This can ensurethat the entire topography 3103 captured by camera 106 is in focus inthe final focus-stacked image.

FIG. 32 illustrates region 3001 sampled by scanner application 204. Thedepths of topography 3103 of specimen 112 can vary along a z-axis 3205.Such variance can create focusing issues. For example, when camera 106is focused on regional peak 3105 of region 3001, other lower areas ofregion 3001 may be out of focus. Conversely, when camera 106 is focusedat maximum depth 3106, then the higher planes in that region can be outof focus. Thus, all image information along z-axis cannot be capturedclearly and accurately in one image by camera.

To address this problem, scanner application 204 can take a plurality ofimages, each at a series of focal planes 3204 orthogonal to z-axis 3205.A sampling distance 3202 can affect both the efficiency and quality of ascan; if sampling distance 3202 is too long, some areas may be out offocus, and if sampling distance 3202 is too short, the scanning willtake an unnecessary amount of time to complete. To determine a preferredsampling distance 3202, scanner application 204 can use variouscalculative methods such as those based on Nyquist sampling frequencyformulas to determine focus planes 3204 along z-axis at which images canbe captured by camera 106. Using Nyquist and one or more characteristicsof light and/or objective lens 107 such as frequency, wavelength, ornumerical aperture. scanner application 204 can calculate a maximumsampling distance (Δzmax) 3201. An example formula for determiningmaximum sampling distance 3201 is

${{\Delta \; z} = \frac{\lambda}{({NA})^{2}}},$

wherein “λ” is wavelength, and “NA” is the numerical aperture.Similarly, scanner application 204 can calculate maximum samplingdistance 3201 using frequency of the light source as well. In onescenario, user can select one or more light settings 2704 to illuminatespecimen 112. In one embodiment, scanner application 204 can samplefocal planes 3204 each separated from nearest adjacent focal plane 3204by sampling distance 3202. In a preferred embodiment, sampling distance3202 of each region can be less than or equal to maximum samplingdistance 3201. Doing so ensures that images in between regional peak3105 and maximum depth 3106 of selected region 3001 can be capturedwithout informational loss from specimen 112. However, sampling distance3202 can be greater than maximum sampling distance 3201 in someembodiments, however such embodiment may have areas that are notcompletely in focus.

In one embodiment, if a user wishes to create and combine multiplescans, each with a different light setting 2704, using varying samplingdistances 3202 for each light setting 2704 can cause each scan to have adifferent number of focal planes 3204 at varying positions along thez-axis. In another embodiment, scanner application 204 can sample eachfocal plane 3204 using sampling distance 3202 of light setting 2704 thathas the shortest wavelength. In such embodiment, each light setting 2704can have the same number of focal planes 3204 at the same positionsalong z-axis 3205.

To perform a scan, scanner processor 201 can send signal to camera 106to capture images at each focal plane 3204. To do so, in one embodiment,scanner application 204 can find regional peak 3105 using interferometer113. Next, camera 106 can focus on focal plane 3204 nearest regionalpeak 3105, by adjusting camera 106, objective lens 107, and/or stage108. Such focal plane 3204 can be chosen such that it is a common focalplane 3204 with adjacent regions 3001. Then camera 106 can shift focusby sampling distance 3202 and capture images of the next lower focalplanes 3204 of selected region 3001. The process of shifting focus andcapturing images on focal plane 3204 at every sampling distance 3202interval can be done repeatedly until reaching focal plane 3204 at orsubstantially near maximum depth 3106 of selected region 3001. Once allfigures in region 3001 are captured, scanner application 204 canfocus-stack images within selected region 3001 into a focus-stacked scan3206.

FIG. 33 illustrates another region 3001 that is sampled by scannerapplication 204. Scanner application 204 can select next region 3001. Inthis region, as interferometer 113 directs a laser down on region 3001,the first reflected signal interferometer 113 receives first can comefrom regional peak 3105, which, in FIG. 33 is lower than top glass slide3101. Next, scanner application 204 can determine focal planes 3204 thatare between regional peak 3105 and maximum depth 3106. Each focal plane3204 can be separated by sampling distance 3202 and can be on commonplanes with focal planes 3204 of FIG. 32. In region 3001 of this figure,scanner processor 201 can send signal to camera 106 to capture images inthe same manner as described in FIG. 32. After images of region 3001 ofthis figure are captured, scanner application 204 can focus-stack theplurality of images into a focus-stacked image. Next, scannerapplication 204 can stitch the focus-stacked image taken from thisselected region 3001 with previously captured images from other regionsto create a complete focus-stacked scan 3206.

FIG. 34 illustrates an exemplary method for scanning specimen 112 forcreating focus-stacked scan 3206. In a preferred method, lens setting2701 can be selected. Next, reflective and/or transmitted light to useon specimen 112 can be chosen. Based on characteristics of the light,maximum sampling distance 3201 can be calculated. In one embodiment,sampling distance 3202 less than or equal to maximum sampling distance3201 can then be chosen. Then, specimen 112 can be divided into regions3001 based on lens setting 2701 selected. For example, a lens withgreater magnification will make visible smaller sections of specimen112. As such, regions 3001 must be smaller. Regional peak 3105 ofselected region 3001 can then be determined using interferometer 113.Next, focal planes 3204 can be determined for selected region 3001.Then, for region 3001, images can be captured between regional peak 3105and maximum depth 3106 at each focal plane 3204. The captured images canbe focus-stacked to create a focus-stacked image. This process can becompleted for each region 3001. Then, focus-stacked images from eachregion 3001 can be stitched to make focus-stacked scan 3206. Theabove-mentioned steps can be repeated for each light setting 2704.

FIG. 35 illustrates another exemplary method for scanning specimen 112for creating focus-stacked scan 3206. In a preferred method, lenssetting 2701 can be selected. Next, one or more light settings 2704,such as reflective and/or transmitted light can be chosen to use onspecimen 112. Based on characteristics of each light, maximum samplingdistance 3201 of the light having the shortest effective wavelength canbe calculated. In one embodiment, sampling distance 3202 less than orequal to maximum sampling distance 3201 can then be chosen. Then,specimen 112 can be divided into regions 3001 based on lens setting 2701selected. For selected region 3001, regional peak 3105 can be determinedusing interferometer 113. Next, each focal plane 3204 between regionalpeak 3105 and maximum depth 3106 can be determined. The space betweeneach focal plane 3204 is less than or equal to maximum sampling distance3201. For focal plane 3204, images can be captured using each lightsetting 2704. This process can be completed for each focal plane 3204 ofselected region 3001. The captured images can be focus-stacked to createa focus-stacked image. The above-mentioned steps can be repeated foreach region 3001 remaining. Then, created focus-stacked images of eachregion 3001 of same light setting 2704 can be stitched intofocus-stacked scans 3206. Lastly, focus-stacked scans, in oneembodiment, can be combined into multi-modal focus-stacked scan 3206.

FIG. 36 illustrates glass slide 111. In this embodiment, specimen 112can be captured and/or defined through a set of focal points 3601. Inone embodiment, a user can select focal points 3601 on specimen 112. Inthis embodiment, the user can manually select each focal point 3601based on the shape and/or region of specimen 112. In another embodiment,scanner application 204 can automatically select focal points 3601 ofspecimen 112. In such embodiment, scanner application 204 can useedge-detection techniques to determine focal points 3601. Further in oneembodiment, focal point 3601 can relate to regional peak 3105. Usinginterferometer 113, scanner application 204 can determine a regionalpeak position 3602 along z-axis 3205 of each focal point 3601 within asubset of regions 3001. Regional peak position 3602 can be thez-coordinate that corresponds to the location of each regional peak3105. Using numerical methods, scanner application 204 can interpolateregional peak positions 3602 of remaining regions 3603 for entirespecimen 112. Numerical methods can include, but are not limited totriangulation, multi-dimensional curve fitting, linear methods andnon-linear methods, parametric and non-parametric methods, as well asregressive techniques.

Scanner application 204 can then direct camera 106 to capture images atregions 3001. During this process, scanner application 204 can ensurethat sampling distance 3202 is less than or equal to maximum samplingdistance 3201 of the selected region 3001. At each light setting 2704,camera 106 can focus on and capture images at focal plane 3204 nearestregional peak 3105 of selected region 3001. Next, camera 106 can focuson a lower focal plane 3204 that is sampling distance (Δz) 3202 awayfrom the interpolated regional peak position 3602. Camera 106 cancapture the images at each focal plane 3204 until camera 106 reachesmaximum depth 3106 on the selected region 3001. In one embodiment, asdescribed here, focal planes 3204 can extend substantially from regionalpeak 3105 to maximum depth 3106 of the selected region 3001. Next,scanner application 204 can determine if there are other regions 3001remaining to be scanned. If there are other regions 3001 left, scannerapplication 204 can move to next region 3001 remaining and begin thesame process of capturing images at various focal planes 3204 betweeninterpolated regional peaks 3105 and maximum depth 3106. After capturingimages at focal planes 3204 for each region 3001 of entire specimen 112,scanner application 204 can focus-stack images of focal planes 3204 withthe same light setting 2704 to create a single focus-stacked image.Next, scanner application 204 can stitch the focus-stacked images takenfrom each region 3001 to create complete focus-stacked scan 3206.

FIG. 37 illustrates another exemplary method for scanning specimen 112for creating focus-stacked scan 3206. In a preferred method, lenssetting 2701 can be selected. Next, light settings 2704 to use onspecimen 112 can be chosen. Then, specimen 112 can be divided intoregions 3001 based on lens setting 2701 selected. Based oncharacteristics of the light, maximum sampling distance 3201 can becalculated. In one embodiment, sampling distance 3202 less than or equalto maximum sampling distance 3201 can then be chosen. Next, focal points3601 can be selected. Regional peak position 3602 at each focal point3601 can be determined using interferometer 113. Then using numericalmethods, regional peaks 3105 can be determined for remaining regions3603. For region 3001, images can be captured at each focal plane 3204from regional peak position 3602 to maximum depth 3106. Captured imagescan be focus-stacked to create a focus-stacked image. This process canbe completed for each region 3001. Then, focus-stacked images of eachregion 3001 of same light setting 2704 can be stitched into one or morefocus-stacked scans 3206.

FIG. 38-42 illustrates multi-dimensional scanning. In amulti-dimensional scan embodiment, images of selected region 3001 can becaptured by camera 106 at different focal planes 3204. Images capturedon common focal planes 3204 can then be stitched together, which canproduce a series of dimensional images at a series of focal planes 3204.

FIG. 38 illustrates focus planes 3204 within specimen 112. In thisembodiment, each region 3001 of entire specimen 112 can be captured froma minimum depth 3801 to maximum depth 3106. Minimum depth 3801 can bethe bottom of top glass slide 3101, in one embodiment. In anotherembodiment, scanner application 204 can determine minimum depth 3801 ofspecimen 112 using interferometer 113 by finding the absolute peak ofspecimen 112. The absolute peak is the portion of specimen 112 closestto camera. Scanner application 204 can then calculate maximum samplingdistance 3201 and a sampling distance 3202 based from light settings2704 used in illuminating selected region 3001. This can ensure imagesin between minimum depth 3801 and maximum depth 3106 of each region 3001can be captured without informational loss from specimen. Specimen 112can be sampled at each focal plane 3204 using camera 106. Each focalplane 3204 can be separated from each adjacent focal plane 3204 bysampling distance 3202. To sample, camera 106 can capture images at eachfocal plane 3204 of the selected region 3001. In one embodiment, camera106 can focus and capture one or more images on focal plane 3204 at ornear minimum depth 3801. Then camera 106 can shift focus and captureimages of the next lower focal plane 3204 of selected region 3001. Theprocess of shifting focus and capturing images on focal plane 3204 atevery sampling distance 3202 interval can be done repeatedly untilreaching focal plane 3204 at or substantially near maximum depth 3106 ofselected region 3001. This process can be repeated for each region 3001of entire specimen 112. In this embodiment, images captured at eachregion 3001 that has same light setting 2704 and same focal plane 3204can be stitched together into one or multi-dimensional scans 3802.

FIG. 39 illustrates an exemplary region illuminated at various lightsettings 2704, sampled with sampling distance 3202 using light setting2704 with shortest wavelength. A user can choose to illuminate specimen112 using multiple light settings 2704. In an example shown in FIG. 39,specimen 112 in region 3001 can be illuminated using multiple lightsettings: a blue light 3901, a white light 3902, and a red light 3903.Scanner application 204 can calculate maximum sampling distance 3201based from each frequency produced by each light setting 2704, or onlyfrom the known highest frequency light. Based from the calculationsmade, scanner application 204 can determine which light source producesthe shortest maximum sampling distance (Δz) 3201. In this example, bluelight 3901 can have the highest frequency followed by the white light3902, and red light 3903 can have the lowest frequency. As such, bluelight 3901 can have the shortest wavelength between the other two lightsettings. Scanner application 204 can then choose sampling distance (Δz)3202 based on maximum sampling distance 3201 of blue light 3901 todetermine focal planes 3204 of the selected region 3001. Therefore, whenselected region 3001 is sampled in red light 3903 and white light 3902,each focal plane 3204 on the selected region 3001 can still use samplingdistance 3202 of blue light 3901, as shown in FIG. 39. A benefit to thisembodiment is that there will be no focal variations when a user viewinga specific region in specimen 112 switches from viewing a scan in onelight setting 2704 to a second light setting 2704. Additionally, lessmechanical movement can be required from stage 108 during scanning sinceimages of specimen 112 are taken at similar z-positions. However, usingthis embodiment can cause over-sampling of a lower frequency lightsetting, which while has no effect on image quality, can cause a scan totake more time.

FIG. 40 illustrates an exemplary region illuminated at various lightsettings 2704, sampled with various sampling distances 3202 relative toeach light setting 2704. In this embodiment, scanner application 204 cancalculate maximum sampling distance 3201 based on each light setting2704 selected. Based from the calculations made, scanner application 204can determine focal planes 3204 to use for each light setting 2704selected. As an example shown in FIG. 40, blue light 3901 that has thehighest frequency can have the shortest wavelength. Thus, whenilluminating region 3001 using blue light 3901, sampling distance 3202between each focal plane 3204 can be shorter. Furthermore, white light3902 having a lower frequency can have longer wavelength than blue light3901. Therefore, when illuminating region 3001 using white light 3902,sampling distance 3202 between each focal plane 3204 can be longer.Lastly, red light 3903 that has the lowest frequency can have thelongest wavelength. As such, when red light 3903 is used in illuminatingregion 3001, sampling distance 3202 between each focal plane 3204 can belongest compared to other two light settings 2704. One of the advantagesin using this embodiment is that it minimizes or eliminatesoversampling. However, in this embodiment, there can be small variationsin focus when a user viewing a specific region in specimen 112 switchesfrom one light setting 2704 to another.

FIG. 41 illustrates an exemplary method for scanning specimen 112 usingmulti-dimensional scanning. In a preferred method, a lens setting 2701can be selected. Next, reflective and/or transmitted light to use onspecimen 112 can be chosen. Then, specimen 112 can be divided intoregions 3001 based on the lens setting 2701 selected. Based oncharacteristics of the light, maximum sampling distance (Δzmax) 3201 canbe calculated. In one embodiment, sampling distance 3202 less than orequal to maximum sampling distance 3201 can then be chosen. For region3001, images can be captured at each focal plane 3204 from minimum depth3801 to maximum depth 3106 using each light setting 2704 selected. Thisprocess can be repeated for each region 3001 of entire specimen 112.Then, images from regions 3001 of the same light setting 2704 and focalplane 3204 can be stitched together into one or more multi-dimensionalscans 3802.

FIG. 42 illustrates another exemplary method for scanning specimen 112at each focal plane 3204 using multi-dimensional scanning. In apreferred method, lens setting 2701 can be selected. Next, lightsettings 2704 to use on specimen 112 can be chosen. Then, specimen 112can be divided into regions 3001 based on lens setting 2701 selected.Based on characteristics of the light, maximum sampling distance 3201can be calculated. In one embodiment, sampling distance 3202 less thanor equal to maximum sampling distance 3201 can then be chosen. Then,minimum depth 3801 can be determined. Next, focal planes 3204 can beselected. For region 3001, images can be captured at each focal point3601 from minimum depth 3801 to maximum depth 3106 separated by samplingdistance 3202. This process can be repeated for each light setting 2704.The above-mentioned steps can be repeated for each region 3001remaining. Then, regions 3001 of the same light setting 2704 and focalplane 3204 can be stitched together into multi-dimensional scans 3802.

FIG. 43 illustrates a pyramidal data structure 4300. In one embodiment,pyramidal data structure 4300 can be a multi-modal and/ormultidimensional pyramidal data structure 4300. In general, tilingdivides an image into a plurality of sub-images. Such division allowseasier buffering of the image data in memory, and quicker random accessof the image data. Pyramidal tiling involves creating a set of low-pass,band-pass or otherwise lower resolution copies of an image. Then each ofthose copies is divided into one or more tiles 4302. One example of adata structure that uses Pyramidal tiling is the JPEG Tiled ImagePyramid (JTIP). A JTIP image stores a plurality of successive layers4301 of the same image at different resolutions. Each layer 4301 istiled, and as the resolution of a layer improves relative to a previouslayer, the number of tiles increases. As described in this disclosure, aplurality of focus-stacked scans 3206 and/or multi-dimensional scans3802 can be stored in pyramidal data structure using a novelpyramidal-tiling technique. Tile 4302 can comprise one or more modes4303. In one embodiment, modes can relate to light settings 2704. Eachmode 4303 can comprise one or more sub-images 4304. In one embodiment,sub-images 4304 can be sequential sub-images of multi-dimensional scans3802.

FIG. 44 illustrates one embodiment of multi-modal pyramidal datastructure 4300. In a first exemplary embodiment, pyramidal datastructure 4300 can be multi-modal, and comprise a plurality offocus-stacked scans 3206. In such embodiment, tiles 4302 can comprise aplurality of modes 4303. Modes 4303 within each tile 4302 can comprisesub-image 4304. As an example, sub-image 4304 a within mode 4303 a canbe a portion of focus-stacked scan 3206 of specimen 112 in blue light,sub-image 4304 b within mode 4303 b can be a portion of focus-stackedscan 3206 of specimen 112 in white light, and sub-image 4304 c withinmode 4303 c can be a portion of focus-stacked scan 3206 of specimen 112in red light. Furthermore, sub-image 4304 a, sub-image 4304 b, andsub-image 4304 c can be images of the same sub-portion of specimen 112.

FIG. 45 illustrates one embodiment of multi-dimensional pyramidal datastructure 4300. In a second exemplary embodiment, pyramidal datastructure 4300 can be multi-dimensional, and comprise multi-dimensionalscan 3802. In such embodiment, tile 4302 can comprise one mode 4303.Mode 4303 can comprise a sequence of sub-images 4304 of amulti-dimensional scan. Each sub-image can be of the same sub-portionsof specimen 112, but focused on a different focal plane 3204.

FIG. 46 illustrates one embodiment of multi-modal multi-dimensionalpyramidal data structure 4300. In a third exemplary embodiment,pyramidal data structure 4300 can be multi-modal and multi-dimensional,comprising a plurality of multi-dimensional scans 3802. In suchembodiment, tile 4302 can comprise multiple modes 4303, each comprisinga sequence of sub-images 4304 from a multidimensional scan. In oneembodiment, each mode 4303 can have the same number of sub-images 4304.For example, mode 4303 a may have been sampled in blue light, mode 4303b in white light, and mode 4303 c in red light. In such embodiment,scanner application 204 may have scanned all three modes 4303 usingsampling distance 3202 related to blue light. In another embodiment,modes 4303 within tile 4302 can have varying numbers of sub-images 4304.This may occur when scanner application 204 scanned different modes 4303using different sampling distances 3202 related to the light settings2704 in the particular mode 4303.

FIG. 47 illustrates another embodiment of multi-modal multi-dimensionalpyramidal data structure 4300. In a fourth exemplary embodiment,pyramidal data structure 4300 can be multi-modal and multi-dimensional,comprising focus-stacked scan 3206 within first mode 4303 a, andmulti-dimensional scans 3802 within second mode 4303 b. In suchembodiment, tile 4302 can comprise sub-image 4304 from focus-stackedscan 3206 and a sequence of sub-images 4304 from multi-dimensional scans3802.

FIG. 48 illustrates a pyramidal file structure 4800 capable of enclosingpyramidal data structure 4300 having one or more modes 4303, and/or aplurality of dimensions (sub-images 4304 within one or more modes 4303).Pyramidal file structure 4800 can comprise a body 4801 and a header4802. Body 4801 can comprise pyramidal data structure 4300. Header 4802can define pyramidal data structure 4300 with a layer plan 4803, a tileplan 4804, a mode plan 4805, and/or a dimension plan 4806. Layer plan4803 can instruct the number of layers within pyramidal data structure4300. In one embodiment, the number indicated on layer plan 4803 can bepredetermined. In another embodiment, a user can set the number oflayers when creating pyramidal file structure 4800. In one embodiment,one or more modes 4303 can be single-layer focus-stacked scan 3206. Inanother embodiment, each mode 4303 can be scanned differently. As such,one mode 4303 can be single-layer focus-stacked scan 3206 while othermodes 4303 within tile 4302 can be multi-dimensional scans 3802. In oneembodiment, dimension plan 4806 can have uniform dimensions resulting inthe same number of sub-images 4304 for each mode 4303, as shown inheader 4802 of FIG. 48. In another embodiment, dimension plan 4806 canhave different dimensions for each scan, resulting in each mode 4303having a different number of sub-images 4304. In one embodiment, header4802 can comprise spacing information, such as sampling distance (Δz)3202 between focal planes 3204 within mode 4303. In another embodiment,XYZ data can be stored in sub-image 4304, along with other settings suchas lens setting 2701, light settings 2704, and/or camera settings.Pyramidal file structure 4800 can be compressed. In one embodiment,pyramidal file structure 4800 can be compressed using waveletcompression.

FIG. 49 illustrates a viewer application allowing user to view scans ofspecimen 112 within pyramidal data structure 4300. In one embodiment,computer application 609 can be a viewer application. In anotherembodiment, server application 604 and/or scanner application 204 can bea viewer application that computer application 609 accesses. Remoteaccess can be in computer data store 610. In one embodiment, viewerapplication can comprise a magnifier 4901, a panning cursor 4902, afocus controller 4903, and a mode selection 4904. Viewer application canread header 4802 to determine what options are available to user tocontrol the viewing of pyramidal data structure 4300. Magnifier 4901 canallow user to zoom in and zoom out the image of specimen 112 on display302. Panning cursor 4902 can allow user to move scan of specimen 112.Focus controller 4903 can allow user to view sub-images 4304 at specificfocal planes 3204 of specimen 112 if pyramidal data structure 4300 ismulti-dimensional. Mode selection 4904 can allow user to select mode4303 to view specimen 112 in if pyramidal data structure 4300 ismulti-modal.

FIG. 50A-D are a sequence of figures that illustrates magnification ofspecimen 112 viewing pyramidal data structure 4300. The user can controlthe magnification of specimen 112 using magnifier 4901.

FIG. 50A illustrates entire specimen 112 being viewed. Using thepyramidal data structure 4300 shown in FIG. 43, top-most layer 4301having the lowest level of resolution relative to the layers, can bedisplayed. At this level, image data of entire specimen 112 can beretrieved from a single tile 4302 in one embodiment.

FIG. 50B illustrates specimen 112 being magnified by adjusting magnifier4901. As specimen 112 is magnified, smaller tile 4302 with higher imageresolution can be retrieved. To keep continuity with focus, sub-image4304 can be chosen such that focal plane 3204 remains constant betweenold and new sub-images 4304.

FIG. 50C illustrates specimen 112 being magnified by further adjustingmagnifier 4901. One advantage scanner 100 has over traditionalmicroscopes is that magnification within viewer application can becontinuous, while under a traditional microscope, magnification isdiscrete and governed by available lenses.

FIG. 50D illustrates specimen 112 being completely magnified by furtheradjusting magnifier 4901 to its maximum position. In one embodiment,when user zooms in all the way, sub-image 4304 on display 302 is aportion of stitched image at its highest resolution. Such sub-image 4304can come from tile 4302 at the bottom layer 4301 of pyramidal datastructure 4300.

FIG. 51 illustrates how image data can be transferred from a localaccess 5101 to a remote access 5102. Specimen 112 can be transferredfrom local access 5101 to remote access 5102 through network 502 to beviewed on display 302 using a viewer application. In one embodiment,local access 5101 can be in server data store 605. In anotherembodiment, local access 5101 can be in scanner data store 205 Each tile4302 of pyramidal data structure 4300 can be stored within local access5101. Tiles 4302 within local access 5101 can be accessed, viewed, andstored within remote access 5102.

As an example scenario, a user at remote access 5102 can initiallychoose to view entire specimen 112 on display 302. In such scenario,remote access 5102 can communicate with local access 5101 to view imagedata of entire specimen 112. Server 501 can then choose the appropriatelayer 4301 and tile 4302 to transfer based on the user's selected areaand/or level of magnification. Since the user chooses to view entirespecimen 112, the top-most layer 4301 having single tile 4302 in thisembodiment can be transferred and stored within remote access 5102, asshown in FIG. 51.

FIG. 52 illustrates magnifying a selected area of specimen 112 on remoteaccess 5102. The user at remote access 5102 can choose to zoom in and/orzoom out of the screen in order to select a specific area of interest onspecimen 112. As a user controls the magnification of the screen, server501 can select the appropriate layer 4301 and tiles 4302 thatcorresponds to the selected view of the user. In this case, as the userselects to magnify the specific area of interest, a portion of the nextlayer 4301 from local access 5101 can be retrieved by remote access5102. To do so, one or more tiles 4302 corresponding to the specificarea selected by the user can be transferred to remote access 5102.

FIG. 53 illustrates fully magnifying a selected area from remote access5102. The user can choose to fully zoom in into a specific area that iswithin the previously displayed image of specimen 112. Based from theselected area of the user, server 501 can choose the appropriate layer4301 and tile 4302 from local access 5101. Server 501 can select tiles4302 from the last layer 4301 to transfer to remote access 5102.

FIG. 54 illustrates selecting a different area to view from remoteaccess 5102. The user can choose to select other areas to view fromremote access 5102. As server 501 transfers a specific tile 4302 andlayer 4301 to remote access 5102, that specific tile 4302 from layer4301 can also be stored within remote access 5102. In FIG. 54, the userchooses to view an area that is adjacent to the previously selectedarea. In this case, as user moves to adjacent area, tile 4302 that isadjacent to the previously tile 4302 can be transferred and stored toremote access 5102.

FIG. 55A-D illustrates adjusting focus controller 4903 and modeselection 4904 in multi-modal multi-dimensional pyramidal data structure4300 on display 302. One purpose of pyramidal data structure 4300 is to,when viewed, imitate viewing specimen 112 under a microscope. To thatend, many controls in viewer application are similar to controls on amicroscope. Just as a user of a microscope can adjust the focus whenviewing a specimen, so too can a user view different focal planes 3204when pyramidal data structure 4300 comprises multi-dimensional scans3802 of specimen 112. Further, just as a user of a microscope can changelight settings 2704, so too can a user view specimen 112 under lightconditions if such light conditions are captured in various modes 4303of multi-modal pyramidal data structure 4300.

FIG. 55A illustrates viewer application viewing sub-image 4304 focusedon focal plane 3204 near region peak 3105. Areas of specimen 112 nearregional peak 3105 will show up as in-focus areas 5501, wherein areasbelow regional peak 3105 will be out-of-focus areas 5502. To adjustfocus, user can use focus controller 4903 to cycle through sub-images4304 of mode 4303, each captured at different, consecutive focal planes3204.

FIG. 55B illustrates a viewer application viewing sub-image 4304 focusedon focal plane 3204 between regional peak 3105 and maximum depth 3106.Areas of specimen 112 near such focal plane 3204 will show up asin-focus areas 5501, wherein areas above and below such focal plane 3204will be out-of-focus areas 5502. To further adjust focus, user can usefocus controller 4903 to further cycle through sub-images 4304.

FIG. 55C illustrates a viewer application viewing sub-image 4304 focusedon focal plane 3204 near maximum depth 3106. Areas of specimen 112 nearmaximum depth 3106 will show up as in-focus areas 5501, wherein areasabove maximum depth 3106 will be out-of-focus areas 5502.

FIG. 55D illustrates a viewer application switching modes 4303 usingmode selection 4904 when viewing multi-modal multi-dimensional pyramidalfile structure 4800 on display 302. In microscopy, sometimes viewingspecimen 112 in particular light settings 2704, such viewing yieldsinformation that may not be visible in other light settings 2704. Whenswitching modes 4303, sub-image 4304 from the new mode 4303 replacessub-image 4304 from the old mode 4303. In a preferred embodiment, bothsub-images 4304 are from a common tile 4202 and on a common focal plane3204. In doing so, the effect for user is that specimen 112 on display302 stays the same, but it appears to be affected only by differences inmode 4303, such as going from white light to blue light, as shown inFIG. 55D.

A number of software components can be stored in scanner memory 202,server memory 602, and computer memory 607 and can be executable byscanner processor 201, server processor 601, and computer processor 606.In this respect, the term “executable” means a program file that is in aform that can ultimately be run by scanner processor 201, serverprocessor 601, and computer processor 606. Examples of executableprograms can be, for example, a compiled program that can be translatedinto machine code in a format that can be loaded into a random accessportion of scanner memory 202, server memory 602, and computer memory607, and run by scanner processor 201, server processor 601, andcomputer processor 606, source code that can be expressed in properformat such as object code that is capable of being loaded into a randomaccess portion of scanner memory 202, server memory 602, and computermemory 607 and executed by scanner processor 201, server processor 601,and computer processor 606, or source code that can be interpreted byanother executable program to generate instructions in a random accessportion of scanner memory 202 to be executed by scanner processor 201,server processor 601, and computer processor 606, etc. An executableprogram can be stored in any portion or component of scanner memory 202,server memory 602, and computer memory 607 including, for example,random access memory (RAM), read-only memory (ROM), hard drive,solid-state drive, USB flash drive, memory card, optical disc such ascompact disc (CD) or digital versatile disc (DVD), floppy disk, magnetictape, or other memory components.

Scanner memory 202, server memory 602, and computer memory 607 isdefined herein as including both volatile and nonvolatile memory anddata storage components. Volatile components are those that do notretain data values upon loss of power. Nonvolatile components are thosethat retain data upon a loss of power. Thus, scanner memory 202, servermemory 602, and computer memory 607 can comprise, for example, randomaccess memory (RAM), read-only memory (ROM), hard disk drives,solid-state drives, USB flash drives, memory cards accessed via a memorycard reader, floppy disks accessed via an associated floppy disk drive,optical discs accessed via an optical disc drive, magnetic tapesaccessed via an appropriate tape drive, and/or other memory components,or a combination of any two or more of these memory components. Inaddition, the RAM can comprise, for example, static random access memory(SRAM), dynamic random access memory (DRAM), or magnetic random accessmemory (MRAM) and other such devices. The ROM can comprise, for example,a programmable read-only memory (PROM), an erasable programmableread-only memory (EPROM), an electrically erasable programmableread-only memory (EEPROM), or other like memory device.

Also, server processor 601, and computer processor 606 can representmultiple, server processor 601, and computer processor 606 and scannermemory 202, server memory 602, and computer memory 607 can representmultiple scanner memory 202, multiple server memory 602, and multiplecomputer memory 607 that operate in parallel processing circuits,respectively. In such a case, first local interface 203, a second localinterface 603, and a third local interface 608 can be an appropriatenetwork, including network 502 that facilitates communication betweenany two of the multiple scanner processor 201, server processor 601, andcomputer processor 606, between any scanner processor 201, serverprocessor 601, and computer processor 606, and any of the scanner memory202, server memory 602, and computer memory 607, or between any two ofthe scanner memory 202, any two of the server memory 602, and any two ofthe computer memory 607, etc. First local interface 203, second localinterface 603, and third local interface 608 can comprise additionalsystems designed to coordinate this communication, including, forexample, performing load balancing. Scanner processor 201, serverprocessor 601, and computer processor 606 can be of electrical or ofsome other available construction.

Although scanner application 204, server application 604, and computerapplication 609, and other various systems described herein can beembodied in software or code executed by general purpose hardware asdiscussed above, as an alternative the same can also be embodied indedicated hardware or a combination of software/general purpose hardwareand dedicated hardware. If embodied in dedicated hardware, each can beimplemented as a circuit or state machine that employs any one of or acombination of a number of technologies. These technologies can include,but are not limited to, discrete logic circuits having logic gates forimplementing various logic functions upon an application of one or moredata signals, application specific integrated circuits havingappropriate logic gates, or other components, etc. Such technologies aregenerally well known by those skilled in the art and, consequently, arenot described in detail herein.

The flowcharts of FIGS. 26, 34, 35, 37, 41 and 42 show the functionalityand operation of an implementation of portions of scanner application204. If embodied in software, each block can represent a module,segment, or portion of code that comprises program instructions toimplement the specified logical function(s). The program instructionscan be embodied in the form of source code that comprises human-readablestatements written in a programming language or machine code thatcomprises numerical instructions recognizable by a suitable executionsystem such as scanner processor 201, server processor 601, and computerprocessor 606 in a computer system or other system. The machine code canbe converted from the source code, etc. If embodied in hardware, eachblock can represent a circuit or a number of interconnected circuits toimplement the specified logical function(s).

Although the flowcharts of FIGS. 26, 34, 35, 37, 41 and 42 show aspecific order of execution, it is understood that the order ofexecution can differ from that which is depicted. For example, the orderof execution of two or more blocks can be scrambled relative to theorder shown. Also, two or more blocks shown in succession in FIGS. 26,34, 35, 37, 41 and 42 can be executed concurrently or with partialconcurrence. In addition, any number of counters, state variables,warning semaphores, or messages might be added to the logical flowdescribed herein, for purposes of enhanced utility, accounting,performance measurement, or providing troubleshooting aids, etc. It isunderstood that all such variations are within the scope of the presentdisclosure.

Also, any logic or application described herein, including scannerapplication 204, server application 602, and computer application 609,that comprises software or code can be embodied in any computer-readablestorage medium for use by or in connection with an instruction executionsystem such as, for example, scanner processor 201, server processor601, and computer processor 606 in a computer system or other system. Inthis sense, the logic can comprise, for example, statements includinginstructions and declarations that can be fetched from thecomputer-readable storage medium and executed by the instructionexecution system.

In the context of the present disclosure, a “computer-readable storagemedium” can be any medium that can contain, store, or maintain the logicor application described herein for use by or in connection with theinstruction execution system. The computer-readable storage medium cancomprise any one of many physical media such as, for example,electronic, magnetic, optical, electromagnetic, infrared, orsemiconductor media. More specific examples of a suitablecomputer-readable storage medium would include, but are not limited to,magnetic tapes, magnetic floppy diskettes, magnetic hard drives, memorycards, solid-state drives, USB flash drives, or optical discs. Also, thecomputer-readable storage medium can be a random access memory (RAM)including, for example, static random access memory (SRAM) and dynamicrandom access memory (DRAM), or magnetic random access memory (MRAM). Inaddition, the computer-readable storage medium can be a read-only memory(ROM), a programmable read-only memory (PROM), an erasable programmableread-only memory (EPROM), an electrically erasable programmableread-only memory (EEPROM), or other type of memory device.

It should be emphasized that the above-described embodiments of thepresent disclosure are merely possible examples of implementations setforth for a clear understanding of the principles of the disclosure.Many variations and modifications can be made to the above-describedembodiment(s) without departing substantially from the spirit andprinciples of the disclosure. All such modifications and variations areintended to be included herein within the scope of this disclosure andprotected by the following claims.

Various changes in the details of the illustrated operational methodsare possible without departing from the scope of the following claims.Some embodiments may combine the activities described herein as beingseparate steps. Similarly, one or more of the described steps may beomitted, depending upon the specific operational environment the methodis being implemented in. It is to be understood that the abovedescription is intended to be illustrative, and not restrictive. Forexample, the above-described embodiments may be used in combination witheach other. Many other embodiments will be apparent to those of skill inthe art upon reviewing the above description. The scope of the inventionshould, therefore, be determined with reference to the appended claims,along with the full scope of equivalents to which such claims areentitled. In the appended claims, the terms “including” and “in which”are used as the plain-English equivalents of the respective terms“comprising” and “wherein.”

1. A method for scanning a specimen into a focus-stacked scan comprisingilluminating a specimen with a light, said specimen comprising atopography, the depths of said topography variable along a z-axis;dividing said specimen into a plurality of regions, each of said regionscomprising a regional peak in said topography; sampling each of saidregions at a plurality of focal planes orthogonal to said z-axis bycapturing, at each focal plane, an image of said region, said imagefocused on said focal plane, focus-stacking, for each said region saidimages within said region, into a focus-stacked image; and stitchingtogether said focus-stacked images into a focus-stacked scan.
 2. Themethod of claim 1 comprising calculating a maximum sampling distance(Δz_(max)) based at least in part on a characteristic of said light,wherein each of said focal planes is separated from each adjacent focalplane by a sampling distance (Δz) less than or equal to said maximumsampling distance.
 3. The method of claim 2 wherein said characteristicis a frequency.
 4. The method of claim 1 further comprising the step ofdetermining within each of said regions a regional peak position alongsaid z-axis of each of said regional peaks, using an interferometer. 5.The method of claim 4 wherein said plurality of focal planes extendssubstantially from said regional peak position to a maximum depth. 6.The method of claim 5 comprising calculating a maximum sampling distance(Δz_(max)) based at least in part on a characteristics of said light,wherein each of said focal planes is separated from each adjacent focalplane by a sampling distance (Δz) less than or equal to said maximumsampling distance.
 7. The method of claim 1 comprising the steps ofchoosing a plurality of said regions; determining within each of saidplurality of said regions a regional peak position along said z-axis ofsaid regional peak, using an interferometer; and estimating by numericalmethods within each of said remaining regions said regional peakposition along said z-axis of said regional peak, said numerical methodsusing said regional peak positions within said plurality of said regionsto estimate regional peak positions of said remaining regions.
 8. Themethod of claim 7 wherein choosing said plurality of said regions isperformed manually.
 9. The method of claim 7 wherein choosing saidplurality of said regions is performed automatically.
 10. The method ofclaim 7 comprising calculating a maximum sampling distance (Δz_(max))based at least in part on a characteristic of said light, wherein eachof said focal planes is separated from each adjacent focal plane by asampling distance (Δz) less than or equal to said maximum samplingdistance.
 11. The method of claim 7 wherein said numerical methodscomprise triangulation.
 12. The method of claim 1 further comprising thesteps illuminating said specimen with a second light, sampling each ofsaid regions at a second plurality of second focal planes orthogonal tosaid z-axis by capturing, at each second focal plane, a second image ofsaid region, said second image focused on said second focal plane, andstitching together said second images focused on a common second focalplane into a second focus-stacked scan.
 13. The method of claim 12comprising the step calculating a second maximum sampling distance(Δz_(max)) based at least in part on a second characteristic of saidsecond light, wherein each of said second focal planes is separated fromeach adjacent second focal plane by a second sampling distance (Δz) lessthan or equal to said second maximum sampling distance.
 14. The methodof claim 1 further comprising the steps illuminating said specimen witha second light, sampling each of said regions at said plurality of focalplanes orthogonal to said z-axis by capturing, at each said focal plane,a second image of said region, said second image focused on said secondfocal plane, and stitching together said second images focused on saidcommon focal plane into a second focus-stacked scan.
 15. 16. The methodof claim 1 wherein said specimen is a petrographic sample.
 17. Aspecimen scanner comprising a camera; a stage capable of supporting aspecimen; a light source capable of illuminating said specimen; ascanner processor; and a scanner memory comprising a scannerapplication, wherein said scanner application directs said scannerprocessor to direct said light source to illuminate said specimen with alight, said specimen comprising a topography, the depths of saidtopography variable along a z-axis; divide said specimen into aplurality of regions, each of said regions comprising a regional peak insaid topography; sample each of said regions at a plurality of focalplanes orthogonal to said z-axis by capturing with said camera, at eachfocal plane, an image of said region, said image focused on said focalplane; focus-stacks, for each said region said images within saidregion, into a focus-stacked image; and stitch together saidfocus-stacked images
 18. The specimen scanner of claim 17 wherein saidstage is capable of moving said specimen along three axes.
 19. Thespecimen scanner of claim 17 wherein said light source comprises areflective light source.
 20. A method for scanning a specimen comprisingthe steps aiming a camera at a plurality of regions of a specimen, oneregion at a time; illuminating said specimen with one or more lights;capturing at each of said regions for each of said lights, at aplurality of focal planes for each focal plane, an image of said region,said image focused on said focal plane; focus-stacking, for each saidregion said images captured with a common light of said one or morelights, within said region, into a focus-stacked image; and stitchingtogether said focus-stacked images captured with said common light. 21.The method of claim 20 wherein aiming said camera comprises adjusting astage that supports said specimen.
 22. The method of claim 20 whereinaiming said camera comprises moving said camera.
 23. The method of claim20 comprising the additional step of changing said focal planes byadjusting the position of a stage.